Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr1
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 35726063
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1821929 characters in sequence are not A, C, G, or T
File 15 of 109
Found at i:5142912 original size:29 final size:30
Alignment explanation
Indices: 5142881--5142944 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
5142871 AATTTCAAAA
* *
5142881 AAAATTAT-AAAACTATTTTTAAA-AATTT
1 AAAATTATAAAAAATATTCTTAAATAATTT
5142909 AAAATTATAAAAAATATTCTTAAATAATTT
1 AAAATTATAAAAAATATTCTTAAATAATTT
*
5142939 TAAATT
1 AAAATT
5142945 CTTTTTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 8 0.26
29 13 0.42
30 10 0.32
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (30 bp):
AAAATTATAAAAAATATTCTTAAATAATTT
Found at i:5142939 original size:40 final size:41
Alignment explanation
Indices: 5142853--5142939 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 41
5142843 GGCATCTAAT
*
5142853 TAATTTTTTAAAATTTAAAATTTCAAAAAAAATTATAAAAC
1 TAATTTTTAAAAATTTAAAATTTCAAAAAAAATTATAAAAC
* * *
5142894 T-ATTTTTAAAAATTTAAAATTAT-AAAAAATATTCTTAAA-
1 TAATTTTTAAAAATTTAAAATT-TCAAAAAAAATTATAAAAC
5142933 TAATTTT
1 TAATTTT
5142940 AAATTCTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
39 1 0.03
40 37 0.93
41 2 0.05
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (41 bp):
TAATTTTTAAAAATTTAAAATTTCAAAAAAAATTATAAAAC
Found at i:5144748 original size:22 final size:22
Alignment explanation
Indices: 5144701--5144749 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
5144691 TATATCTAAC
5144701 ATTTAGAATTTTGATTTCATAG
1 ATTTAGAATTTTGATTTCATAG
5144723 -TTTAGAATTTTTGGATTT-A-AG
1 ATTTAGAA-TTTT-GATTTCATAG
5144744 ATTTAG
1 ATTTAG
5144750 GATTATTGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
21 9 0.38
22 10 0.42
23 5 0.21
ACGTcount: A:0.31, C:0.02, G:0.16, T:0.51
Consensus pattern (22 bp):
ATTTAGAATTTTGATTTCATAG
Found at i:5146672 original size:24 final size:23
Alignment explanation
Indices: 5146645--5146707 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 23
5146635 GATTTGTCCT
5146645 TTTTTATT-TTTCTTTCATTTTAAG
1 TTTTTATTATTTCTTT--TTTTAAG
5146669 TTTTTATTTATTTACTTTTTTTAAG
1 TTTTTA-TTATTT-CTTTTTTTAAG
*
5146694 TTTTTTTTATTTCT
1 TTTTTATTATTTCT
5146708 CCTTATTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
23 2 0.06
24 12 0.34
25 14 0.40
26 3 0.09
27 4 0.11
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.75
Consensus pattern (23 bp):
TTTTTATTATTTCTTTTTTTAAG
Found at i:5146672 original size:25 final size:24
Alignment explanation
Indices: 5146644--5146707 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 24
5146634 TGATTTGTCC
5146644 TTTTTTATT-TTTCTTTCATTTTAAG
1 TTTTTTATTATTTCTTT--TTTTAAG
5146669 -TTTTTATTTATTTACTTTTTTTAAG
1 TTTTTTA-TTATTT-CTTTTTTTAAG
5146694 TTTTTT-TTATTTCT
1 TTTTTTATTATTTCT
5146708 CCTTATTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
23 2 0.06
24 12 0.34
25 9 0.26
26 8 0.23
27 4 0.11
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.75
Consensus pattern (24 bp):
TTTTTTATTATTTCTTTTTTTAAG
Found at i:5146678 original size:4 final size:4
Alignment explanation
Indices: 5146671--5146747 Score: 50
Period size: 4 Copynumber: 18.5 Consensus size: 4
5146661 ATTTTAAGTT
* * *
5146671 TTTA TTTA TTTA CTTTT TTTAA GTT- TTT- TTTA TTTC TCCTTA TTTA
1 TTTA TTTA TTTA -TTTA TTT-A TTTA TTTA TTTA TTTA T--TTA TTTA
* *
5146717 TTTA TTTTA TTTA TTTG TTTA TTTG TTTA TT
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TT
5146748 ATTGGTTTTG
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
3 5 0.09
4 40 0.70
5 9 0.16
6 3 0.05
ACGTcount: A:0.17, C:0.05, G:0.04, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:5149682 original size:30 final size:30
Alignment explanation
Indices: 5149641--5149773 Score: 135
Period size: 30 Copynumber: 4.4 Consensus size: 30
5149631 GTCGCAGAGC
* *
5149641 AGTTCACATCACCTGGACATGGGTGGTTCA
1 AGTTCATATCACCTGGACATGGGTGGTTCG
* *
5149671 AGTTCATATCACCCGGACATGGGCTGCTT-G
1 AGTTCATATCACCTGGACATGGG-TGGTTCG
* *
5149701 AGTTCATATCACCTGGATATGGGTGATTCG
1 AGTTCATATCACCTGGACATGGGTGGTTCG
* * *
5149731 ATTTCATATCA-CTCGGACATAGGCGGTTCG
1 AGTTCATATCACCT-GGACATGGGTGGTTCG
* *
5149761 AGTTTATTTCACC
1 AGTTCATATCACC
5149774 CAGAGCAACC
Statistics
Matches: 84, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
29 6 0.07
30 73 0.87
31 5 0.06
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.31
Consensus pattern (30 bp):
AGTTCATATCACCTGGACATGGGTGGTTCG
Found at i:5149773 original size:60 final size:60
Alignment explanation
Indices: 5149641--5149754 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
5149631 GTCGCAGAGC
* * *
5149641 AGTTCACATCACCTGGACATGGGTGGTTCAAGTTCATATCACCCGGACATGGGCTGCTTG
1 AGTTCATATCACCTGGACATGGGTGATTCAAGTTCATATCACCCGGACATAGGCTGCTTG
* * * *
5149701 AGTTCATATCACCTGGATATGGGTGATTCGATTTCATATCACTCGGACATAGGC
1 AGTTCATATCACCTGGACATGGGTGATTCAAGTTCATATCACCCGGACATAGGC
5149755 GGTTCGAGTT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.29
Consensus pattern (60 bp):
AGTTCATATCACCTGGACATGGGTGATTCAAGTTCATATCACCCGGACATAGGCTGCTTG
Found at i:5152801 original size:24 final size:24
Alignment explanation
Indices: 5152750--5152802 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
5152740 GGACAAATAA
* *
5152750 AAAAACTTAAAAAAGTAAATAAAT
1 AAAAACTTAAAAAAGAAAAAAAAT
5152774 AAAAACTT-AAAAAGAAAAAAAAT
1 AAAAACTTAAAAAAGAAAAAAAAT
5152797 GAAAAA
1 -AAAAA
5152803 GGACAAAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 13 0.50
24 13 0.50
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.15
Consensus pattern (24 bp):
AAAAACTTAAAAAAGAAAAAAAAT
Found at i:5169331 original size:3 final size:3
Alignment explanation
Indices: 5169325--5169351 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5169315 GATGATGACT
5169325 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
5169352 AAGTCTAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5178547 original size:2 final size:2
Alignment explanation
Indices: 5178504--5178528 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5178494 AAGGGGAGGG
5178504 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
5178529 GAGGAAACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5181319 original size:25 final size:24
Alignment explanation
Indices: 5181272--5181323 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
5181262 GTCATTAGGG
* *
5181272 TTACCGATTCTAGCTCTTATGAGC
1 TTACCGATACTAGCTCGTATGAGC
*
5181296 TTACCGATACTCAGCTCGTGTGAGC
1 TTACCGATACT-AGCTCGTATGAGC
5181321 TTA
1 TTA
5181324 TCGTTATTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (24 bp):
TTACCGATACTAGCTCGTATGAGC
Found at i:5181338 original size:25 final size:25
Alignment explanation
Indices: 5181291--5181338 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
5181281 CTAGCTCTTA
*
5181291 TGAGCTTACCGATACTCAGCTCGTG
1 TGAGCTTACCGATACTCAACTCGTG
* * *
5181316 TGAGCTTATCGTTATTCAACTCG
1 TGAGCTTACCGATACTCAACTCG
5181339 GAGGAGCTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.33
Consensus pattern (25 bp):
TGAGCTTACCGATACTCAACTCGTG
Found at i:5185784 original size:19 final size:20
Alignment explanation
Indices: 5185742--5185784 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
5185732 AAAGGTAAGT
* *
5185742 GTTTTTATATATTTTTTATA
1 GTTTTTATATATTATATATA
5185762 -TTTTTATATA-TATATATA
1 GTTTTTATATATTATATATA
5185780 GTTTT
1 GTTTT
5185785 ATTTTAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (20 bp):
GTTTTTATATATTATATATA
Found at i:5185900 original size:40 final size:40
Alignment explanation
Indices: 5185855--5185932 Score: 156
Period size: 40 Copynumber: 1.9 Consensus size: 40
5185845 GTAAAAAAGA
5185855 AAAGACCTTTTGAACGTTTTTTACTTCTCTTCTCTCTGCT
1 AAAGACCTTTTGAACGTTTTTTACTTCTCTTCTCTCTGCT
5185895 AAAGACCTTTTGAACGTTTTTTACTTCTCTTCTCTCTG
1 AAAGACCTTTTGAACGTTTTTTACTTCTCTTCTCTCTG
5185933 TTTTGTCACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.18, C:0.24, G:0.10, T:0.47
Consensus pattern (40 bp):
AAAGACCTTTTGAACGTTTTTTACTTCTCTTCTCTCTGCT
Found at i:5187733 original size:52 final size:54
Alignment explanation
Indices: 5187670--5187873 Score: 210
Period size: 52 Copynumber: 3.9 Consensus size: 54
5187660 ACTGGCCACA
* * * *
5187670 ACCCTAAATTTTTTT-A-TCT-GATAAAGGGTTGTCAGCCATCAGTGTCTCAAT
1 ACCCAAAATTTTTTTAATTCTAGATAAAGGGGTGTCAGCCATCAGTGTCCCAGT
* * * *
5187721 ACCCCAAAATTTTTTTAATTCTGGA-AAAGAGGT-TCTAACCATCAGTGCCCCAGT
1 A-CCCAAAATTTTTTTAATTCTAGATAAAGGGGTGTC-AGCCATCAGTGTCCCAGT
* * *
5187775 ACCCAAAATTTTTTTAA-T-TAGATAAAGGGGTGTCGGCCATTAGTGTCCCAGC
1 ACCCAAAATTTTTTTAATTCTAGATAAAGGGGTGTCAGCCATCAGTGTCCCAGT
* *
5187827 ACCCAAAATTTTTTT-ATTC-AGATAAAGGGGTGCCGGCCATCAGTGTC
1 ACCCAAAATTTTTTTAATTCTAGATAAAGGGGTGTCAGCCATCAGTGTC
5187874 ATGACACCCC
Statistics
Matches: 128, Mismatches: 16, Indels: 17
0.80 0.10 0.11
Matches are distributed among these distances:
51 5 0.04
52 76 0.59
53 21 0.16
54 24 0.19
55 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (54 bp):
ACCCAAAATTTTTTTAATTCTAGATAAAGGGGTGTCAGCCATCAGTGTCCCAGT
Found at i:5187882 original size:52 final size:50
Alignment explanation
Indices: 5187641--5187873 Score: 166
Period size: 52 Copynumber: 4.5 Consensus size: 50
5187631 TCGAAATACA
* * * *
5187641 AAAGGGGTGTCGGCCATGCACTGGCCA-CAACCCTAAATTTTTTTATCT-GAT
1 AAAGGGGTGCCGGCCAT-CAGTGTCCAGC-ACCCAAAATTTTTTTAT-TAGAT
* * * ** *
5187692 AAAGGGTTGTCAGCCATCAGTGTCTCAATACCCCAAAATTTTTTTAATTCTGGA-
1 AAAGGGGTGCCGGCCATCAGTGTC-CAGCA-CCCAAAATTTTTTT-A-T-TAGAT
* * *** * *
5187746 AAAGAGGTTCTAACCATCAGTGCCCCAGTACCCAAAATTTTTTTAATTAGAT
1 AAAGGGGTGCCGGCCATCAGTG-TCCAGCACCCAAAATTTTTTT-ATTAGAT
* *
5187798 AAAGGGGTGTCGGCCATTAGTGTCCCAGCACCCAAAATTTTTTTATTCAGAT
1 AAAGGGGTGCCGGCCATCAGTGT-CCAGCACCCAAAATTTTTTTATT-AGAT
5187850 AAAGGGGTGCCGGCCATCAGTGTC
1 AAAGGGGTGCCGGCCATCAGTGTC
5187874 ATGACACCCC
Statistics
Matches: 146, Mismatches: 26, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
50 5 0.03
51 25 0.17
52 73 0.50
53 17 0.12
54 23 0.16
55 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (50 bp):
AAAGGGGTGCCGGCCATCAGTGTCCAGCACCCAAAATTTTTTTATTAGAT
Found at i:5187891 original size:52 final size:50
Alignment explanation
Indices: 5187759--5187894 Score: 148
Period size: 52 Copynumber: 2.6 Consensus size: 50
5187749 GAGGTTCTAA
* * * *
5187759 CCATCAGTGCCCCAGTACCCAAAATTTTTTTAATTAGATAAAGGGGTGTCGG
1 CCATCAGTG-TCCAGCACCC-AAATTTTTTTTATTAGATAAAGGGGTGCCGG
* *
5187811 CCATTAGTGTCCCAGCACCCAAAATTTTTTTATTCAGATAAAGGGGTGCCGG
1 CCATCAGTGT-CCAGCACCCAAATTTTTTTTATT-AGATAAAGGGGTGCCGG
*
5187863 CCATCAGTGT-CATGACACCCCAATTTTTTTTA
1 CCATCAGTGTCCA-G-CACCCAAATTTTTTTTA
5187895 AATATACCAG
Statistics
Matches: 71, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
50 2 0.03
51 13 0.18
52 56 0.79
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (50 bp):
CCATCAGTGTCCAGCACCCAAATTTTTTTTATTAGATAAAGGGGTGCCGG
Found at i:5188950 original size:25 final size:27
Alignment explanation
Indices: 5188906--5188967 Score: 103
Period size: 25 Copynumber: 2.4 Consensus size: 27
5188896 ATAAAAAATA
5188906 ACCAAAATAT-TATAATTTTTTTATTT
1 ACCAAAATATATATAATTTTTTTATTT
5188932 ACCAAAATATATAT-A-TTTTTTATTT
1 ACCAAAATATATATAATTTTTTTATTT
5188957 ACCAAAATATA
1 ACCAAAATATA
5188968 CTAAAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
25 21 0.60
26 11 0.31
27 3 0.09
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.47
Consensus pattern (27 bp):
ACCAAAATATATATAATTTTTTTATTT
Found at i:5189141 original size:4 final size:4
Alignment explanation
Indices: 5189132--5189267 Score: 70
Period size: 4 Copynumber: 33.0 Consensus size: 4
5189122 GAAGGAGAGG
* *
5189132 GAAA GAAA GAAA GAAA GAAA GAAA GGAATGA GAAA AAAA GAAGA AAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA -GAA--A GAAA GAAA GAA-A GAAA
* * *
5189180 GAAG GAAA GAAAA GGAAA G-GA GAAGA GAAA -AAA -AAA GGAA G-AA GAAGA
1 GAAA GAAA G-AAA -GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAA-A
*
5189228 GGAAA GGAGAA GAAA -AAA GAAA G-AA -AAA GAAG GAAA GAAA
1 -GAAA -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
5189268 AGGAGAGGAG
Statistics
Matches: 105, Mismatches: 11, Indels: 32
0.71 0.07 0.22
Matches are distributed among these distances:
3 18 0.17
4 54 0.51
5 23 0.22
6 9 0.09
7 1 0.01
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:5189165 original size:27 final size:27
Alignment explanation
Indices: 5189135--5189186 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
5189125 GGAGAGGGAA
* *
5189135 AGAAAGAAAGAA-AGAAAGAAAGGAATG
1 AGAAAAAAAGAAGAAAAAG-AAGGAATG
5189162 AGAAAAAAAGAAGAAAAAGAAGGAA
1 AGAAAAAAAGAAGAAAAAGAAGGAA
5189187 AGAAAAGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (27 bp):
AGAAAAAAAGAAGAAAAAGAAGGAATG
Found at i:5189175 original size:3 final size:3
Alignment explanation
Indices: 5189169--5189307 Score: 50
Period size: 3 Copynumber: 49.3 Consensus size: 3
5189159 ATGAGAAAAA
* * * *
5189169 AAG AAG AAA AAG AAG GA- AAG AA- AAG GA- AAG GAG AAG -AG AA- AA-
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * * *
5189211 AAA AAG GAAG AAG AAG AGG AAAG GAG AAG AA- AA- AAG AAAG AAA AAG
1 AAG AAG -AAG AAG AAG AAG -AAG AAG AAG AAG AAG AAG -AAG AAG AAG
* * * * *
5189257 AAG GA- AAG AA- AAG GAG -AG GAG AAG -AG AAA AAA AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
5189301 AAG AAG A
1 AAG AAG A
5189308 GGGAAGGAAA
Statistics
Matches: 102, Mismatches: 21, Indels: 26
0.68 0.14 0.17
Matches are distributed among these distances:
2 21 0.21
3 73 0.72
4 8 0.08
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:5189187 original size:10 final size:10
Alignment explanation
Indices: 5189166--5189263 Score: 65
Period size: 10 Copynumber: 9.3 Consensus size: 10
5189156 GGAATGAGAA
5189166 AAAAAGAA-G
1 AAAAAGAAGG
5189175 AAAAAGAAGG
1 AAAAAGAAGG
5189185 AAAGAA-AAGG
1 AAA-AAGAAGG
*
5189195 AAAGGAGAAGAG
1 AAA-AAGAAG-G
*
5189207 AAAAAAAAAGG
1 -AAAAAGAAGG
*
5189218 AAGAAGAAGAGG
1 AAAAAG-A-AGG
* *
5189230 AAAGGAGAAGA
1 AAA-AAGAAGG
*
5189241 AAAAAGAAAG
1 AAAAAGAAGG
5189251 AAAAAGAAGG
1 AAAAAGAAGG
5189261 AAA
1 AAA
5189264 GAAAAGGAGA
Statistics
Matches: 69, Mismatches: 12, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
9 8 0.12
10 33 0.48
11 12 0.17
12 11 0.16
13 5 0.07
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
AAAAAGAAGG
Found at i:5189225 original size:35 final size:35
Alignment explanation
Indices: 5189175--5189335 Score: 147
Period size: 35 Copynumber: 4.5 Consensus size: 35
5189165 AAAAAAGAAG
5189175 AAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAA
1 AAAAAGAA-G-AAGAAAAGGAAAGGAGAAGAGAAAAA
* * *
5189212 AAAAGGAAGAAGAAGAGGAAAGGAGAAGAAAAAAGAAA
1 AAAAAGAAGAAGAAAAGGAAAGGAGAAG--AGAA-AAA
*
5189250 GAAAAAGAAGGAAAGAAAAGGAGAGGAGAAGAG--AAA
1 -AAAAAGAA-G-AAGAAAAGGAAAGGAGAAGAGAAAAA
5189286 AAAAAGAAGAAGAAGAA-GAAGAGG-GAAG-GAAAAA
1 AAAAAGAAGAAGAA-AAGGAA-AGGAGAAGAGAAAAA
5189320 AAAAAGAA-AA-AAAAGG
1 AAAAAGAAGAAGAAAAGG
5189336 TAATTTTTTT
Statistics
Matches: 105, Mismatches: 8, Indels: 27
0.75 0.06 0.19
Matches are distributed among these distances:
31 2 0.02
32 4 0.04
33 13 0.12
34 17 0.16
35 26 0.25
36 4 0.04
37 10 0.10
38 3 0.03
39 8 0.08
40 1 0.01
41 17 0.16
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (35 bp):
AAAAAGAAGAAGAAAAGGAAAGGAGAAGAGAAAAA
Found at i:5189252 original size:76 final size:75
Alignment explanation
Indices: 5189165--5189335 Score: 258
Period size: 75 Copynumber: 2.3 Consensus size: 75
5189155 AGGAATGAGA
*
5189165 AAAAAAG-AAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAGGAAGAAGAAGAG
1 AAAAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAG-AAAAAAAA-GAAGAAGAAGAA
5189229 GAA-AGGAGAA-G
64 GAAGAGG-GAAGG
*
5189240 AAAAAAGAAAGAAAAAGAAGGAAAGAAAAGGAGAGGAGAAGAGAAAAAAAAGAAGAAGAAGAAGA
1 AAAAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAGAAGAAGAAGAAGA
5189305 AGAGGGAAGG
66 AGAGGGAAGG
* *
5189315 AAAAAAAAAAGAAAAAAAAGG
1 AAAAAAGAAAGAAAAAGAAGG
5189336 TAATTTTTTT
Statistics
Matches: 89, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
74 17 0.19
75 38 0.43
76 34 0.38
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (75 bp):
AAAAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAGAAGAAGAAGAAGA
AGAGGGAAGG
Found at i:5190316 original size:69 final size:69
Alignment explanation
Indices: 5190221--5190362 Score: 275
Period size: 69 Copynumber: 2.1 Consensus size: 69
5190211 TATGTTAAGA
5190221 AATAAATTAATAAAGACAAATGTATGGCGATATTTAAGACAAGTGTATTAATAAAATACATACAT
1 AATAAATTAATAAAGACAAATGTATGGCGATATTTAAGACAAGTGTATTAATAAAATACATACAT
5190286 TTGT
66 TTGT
*
5190290 AATAAATTAATAAAGACAAATGTATGGTGATATTTAAGACAAGTGTATTAATAAAATACATACAT
1 AATAAATTAATAAAGACAAATGTATGGCGATATTTAAGACAAGTGTATTAATAAAATACATACAT
5190355 TTGT
66 TTGT
5190359 AATA
1 AATA
5190363 CTTATATGTA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 72 1.00
ACGTcount: A:0.49, C:0.06, G:0.13, T:0.32
Consensus pattern (69 bp):
AATAAATTAATAAAGACAAATGTATGGCGATATTTAAGACAAGTGTATTAATAAAATACATACAT
TTGT
Found at i:5190470 original size:17 final size:17
Alignment explanation
Indices: 5190426--5190460 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5190416 AGTTAAAATA
*
5190426 AAAAGAATAAAAGAAAC
1 AAAAGAAGAAAAGAAAC
5190443 AAAAGAAGAAAAGAAAC
1 AAAAGAAGAAAAGAAAC
5190460 A
1 A
5190461 GAATAGGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.77, C:0.06, G:0.14, T:0.03
Consensus pattern (17 bp):
AAAAGAAGAAAAGAAAC
Found at i:5191194 original size:12 final size:12
Alignment explanation
Indices: 5191179--5191209 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5191169 TAGTATTAAT
5191179 TTATTATTAGCA
1 TTATTATTAGCA
*
5191191 TTATTATTAGTA
1 TTATTATTAGCA
5191203 TTATTAT
1 TTATTAT
5191210 GAGTGGGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.58
Consensus pattern (12 bp):
TTATTATTAGCA
Found at i:5191377 original size:23 final size:24
Alignment explanation
Indices: 5191351--5191396 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
5191341 GTGTGAATTT
* *
5191351 GTGAAATAATTATTG-ATTGAAAG
1 GTGAAAAAATGATTGAATTGAAAG
5191374 GTGAAAAAATGATTGAATTGAAA
1 GTGAAAAAATGATTGAATTGAAA
5191397 ATGTGAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.48, C:0.00, G:0.22, T:0.30
Consensus pattern (24 bp):
GTGAAAAAATGATTGAATTGAAAG
Found at i:5192651 original size:27 final size:27
Alignment explanation
Indices: 5192621--5192676 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
5192611 AAAGAGGGTG
*
5192621 ATGGAGGGGAATAAAAAGGCGGCACCA
1 ATGGAGAGGAATAAAAAGGCGGCACCA
5192648 ATGGAGAGGAATAAAAAGGCGGCACCA
1 ATGGAGAGGAATAAAAAGGCGGCACCA
5192675 AT
1 AT
5192677 ATGTGGCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.43, C:0.14, G:0.34, T:0.09
Consensus pattern (27 bp):
ATGGAGAGGAATAAAAAGGCGGCACCA
Found at i:5196888 original size:3 final size:3
Alignment explanation
Indices: 5196880--5196911 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5196870 TCTTAATACT
5196880 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
5196912 TAATAATACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:5197054 original size:10 final size:11
Alignment explanation
Indices: 5197037--5197065 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
5197027 TAAAAAATAC
5197037 CTTCTTTTTCT
1 CTTCTTTTTCT
5197048 C-TCTTTTTCT
1 CTTCTTTTTCT
5197058 CTTCTTTT
1 CTTCTTTT
5197066 CCACAGCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (11 bp):
CTTCTTTTTCT
Found at i:5197265 original size:27 final size:27
Alignment explanation
Indices: 5197227--5197287 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
5197217 TTTTTTTGGT
*
5197227 ATATTTTGGTAAATAAAAAAAATTATA
1 ATATTTTAGTAAATAAAAAAAATTATA
*
5197254 ATATTTTAGTAAATAAAAAAAGTTATA
1 ATATTTTAGTAAATAAAAAAAATTATA
5197281 ATATTTT
1 ATATTTT
5197288 GGTTATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (27 bp):
ATATTTTAGTAAATAAAAAAAATTATA
Found at i:5197812 original size:30 final size:30
Alignment explanation
Indices: 5197776--5197832 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
5197766 CTTTTTTTGC
* * *
5197776 TGTTTTTTTATTATTTTGTTGCTATTTTCT
1 TGTTTTTTCACTATTTTGTTACTATTTTCT
5197806 TGTTTTTTCACTATTTTGTTACTATTT
1 TGTTTTTTCACTATTTTGTTACTATTT
5197833 CACAATTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.12, C:0.09, G:0.09, T:0.70
Consensus pattern (30 bp):
TGTTTTTTCACTATTTTGTTACTATTTTCT
Found at i:5203221 original size:15 final size:15
Alignment explanation
Indices: 5203191--5203230 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
5203181 TATGTTAACT
5203191 TAATATATATAAGTTA
1 TAATA-ATATAAGTTA
*
5203207 TAATAATATATGTTA
1 TAATAATATAAGTTA
5203222 TAATAATAT
1 TAATAATAT
5203231 TTAAAACATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (15 bp):
TAATAATATAAGTTA
Found at i:5205911 original size:20 final size:19
Alignment explanation
Indices: 5205865--5205903 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
5205855 AATTTTAAAA
*
5205865 TATTTTAAAAATATTTTTT
1 TATTTTTAAAATATTTTTT
5205884 TATTTTTAAAATATTTTTT
1 TATTTTTAAAATATTTTTT
5205903 T
1 T
5205904 TGTGTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TATTTTTAAAATATTTTTT
Found at i:5206200 original size:49 final size:49
Alignment explanation
Indices: 5206128--5206221 Score: 170
Period size: 49 Copynumber: 1.9 Consensus size: 49
5206118 TCAAGAAGGG
**
5206128 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGATTAAGTTTAGCAATGT
1 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACCAAGTTTAGCAATGT
5206177 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACCAAGTTTAGCA
1 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACCAAGTTTAGCA
5206222 TTGCATAGCA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.41, C:0.06, G:0.27, T:0.26
Consensus pattern (49 bp):
ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACCAAGTTTAGCAATGT
Found at i:5206800 original size:25 final size:25
Alignment explanation
Indices: 5206755--5206863 Score: 147
Period size: 23 Copynumber: 4.6 Consensus size: 25
5206745 ATCAAATCAA
*
5206755 ACAGCAT-T-TATACACCCAATTGG
1 ACAGCATATATATACACCAAATTGG
*
5206778 ACAGCATATATATATACCAAATTGG
1 ACAGCATATATATACACCAAATTGG
*
5206803 ACAGC--ATATATACACTAAATTGG
1 ACAGCATATATATACACCAAATTGG
*
5206826 ACAGCAT-TTTATACACCAAATTGG
1 ACAGCATATATATACACCAAATTGG
5206850 ACAGCATATATATA
1 ACAGCATATATATA
5206864 TACTCAATCA
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
23 28 0.38
24 23 0.31
25 23 0.31
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (25 bp):
ACAGCATATATATACACCAAATTGG
Found at i:5206815 original size:48 final size:47
Alignment explanation
Indices: 5206755--5206861 Score: 160
Period size: 47 Copynumber: 2.3 Consensus size: 47
5206745 ATCAAATCAA
* * *
5206755 ACAGCATTTATACACCCAATTGGACAGCATATATATATACCAAATTGG
1 ACAGCATATATACACCAAATTGGACAGCAT-TATATACACCAAATTGG
* *
5206803 ACAGCATATATACACTAAATTGGACAGCATTTTATACACCAAATTGG
1 ACAGCATATATACACCAAATTGGACAGCATTATATACACCAAATTGG
5206850 ACAGCATATATA
1 ACAGCATATATA
5206862 TATACTCAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
47 27 0.50
48 27 0.50
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (47 bp):
ACAGCATATATACACCAAATTGGACAGCATTATATACACCAAATTGG
Found at i:5206924 original size:2 final size:2
Alignment explanation
Indices: 5206917--5206949 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5206907 ATGTCATACT
5206917 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5206950 GAAACTCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5208181 original size:43 final size:42
Alignment explanation
Indices: 5208125--5208253 Score: 138
Period size: 43 Copynumber: 3.0 Consensus size: 42
5208115 ATATCGTATA
*
5208125 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATAACG
1 ATGCCAACATCCCAGACGTGGTCTTACATGTAA-CACATAACG
**
5208168 ATGCC-ACTATCCCAGACAG-GGTCTTACATGTAAACACA-AGTTG
1 ATGCCAAC-ATCCCAGAC-GTGGTCTTACATGT-AACACATA-ACG
* *
5208211 ATGCCAACGTCCCAGACGTGGTCTTACATGATAACATATAACG
1 ATGCCAACATCCCAGACGTGGTCTTACATG-TAACACATAACG
5208254 GAATCCTATG
Statistics
Matches: 71, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
42 4 0.06
43 60 0.85
44 7 0.10
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (42 bp):
ATGCCAACATCCCAGACGTGGTCTTACATGTAACACATAACG
Found at i:5209379 original size:13 final size:13
Alignment explanation
Indices: 5209361--5209385 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5209351 CTCAAACAAT
5209361 AAATTTTCACACG
1 AAATTTTCACACG
5209374 AAATTTTCACAC
1 AAATTTTCACAC
5209386 ATATTGATTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:5211084 original size:51 final size:50
Alignment explanation
Indices: 5210919--5211101 Score: 206
Period size: 51 Copynumber: 3.6 Consensus size: 50
5210909 AGTGAAAGTG
*
5210919 ATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGGT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG-ATGGT
* * * * ** * *
5210970 A-GGTCGCATGTATAGTACTATGTGTAGGCTACTATGCATACCAGATAGT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGT
* * * * *
5211019 TTCGATCACGTGTGTAGTACTATGTACAGGCTACTACGTGTATCGGATGGT
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGT
5211070 AATGGTCACATGTGTAGTACTATGTGCAGGCT
1 -ATGGTCACATGTGTAGTACTATGTGCAGGCT
5211102 GCTATGTGAA
Statistics
Matches: 103, Mismatches: 26, Indels: 6
0.76 0.19 0.04
Matches are distributed among these distances:
49 4 0.04
50 35 0.34
51 63 0.61
52 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (50 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGT
Found at i:5211167 original size:45 final size:45
Alignment explanation
Indices: 5211116--5211203 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 45
5211106 TGTGAACCGA
* * * *
5211116 ACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCCACCAG
1 ACATCATTAATTAATAAGGTGGTTACTATGTGCTGAATCCACCAG
*
5211161 ACATCATTAATTAATAATGTGGTTACTATGTGCTGAATCCACC
1 ACATCATTAATTAATAAGGTGGTTACTATGTGCTGAATCCACC
5211204 GAGTATCTGT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.34
Consensus pattern (45 bp):
ACATCATTAATTAATAAGGTGGTTACTATGTGCTGAATCCACCAG
Found at i:5214372 original size:22 final size:24
Alignment explanation
Indices: 5214328--5214378 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
5214318 TATTAATTTT
5214328 AAAATAATAATAGAATAATAATAA
1 AAAATAATAATAGAATAATAATAA
5214352 AAAATAA-AATCAGAA-AA-AATAA
1 AAAATAATAAT-AGAATAATAATAA
5214374 AAAAT
1 AAAAT
5214379 TTAATAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 10 0.38
23 5 0.19
24 11 0.42
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.20
Consensus pattern (24 bp):
AAAATAATAATAGAATAATAATAA
Found at i:5214453 original size:30 final size:29
Alignment explanation
Indices: 5214384--5214461 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
5214374 AAAATTTAAT
5214384 AATTACATTTT-AGCCCTAACTTTTTCAAA
1 AATTACATTTTGA-CCCTAACTTTTTCAAA
* *
5214413 AATTATATTTTGACCCTAACTTTTCCTC-TA
1 AATTACATTTTGACCCTAACTTTT--TCAAA
*
5214443 AATTACATTTTGGCCCTAA
1 AATTACATTTTGACCCTAA
5214462 GAGTTTTGCA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 21 0.50
30 19 0.45
31 2 0.05
ACGTcount: A:0.31, C:0.22, G:0.05, T:0.42
Consensus pattern (29 bp):
AATTACATTTTGACCCTAACTTTTTCAAA
Found at i:5215054 original size:17 final size:18
Alignment explanation
Indices: 5215022--5215056 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5215012 AGAGTTTTGA
5215022 AAAAAAAGAGTAGGGAAAG
1 AAAAAAAGAG-AGGGAAAG
5215041 AAAAAAAGAG-GGGAAA
1 AAAAAAAGAGAGGGAAA
5215057 CACCGGTAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
19 10 0.62
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.03
Consensus pattern (18 bp):
AAAAAAAGAGAGGGAAAG
Found at i:5215172 original size:17 final size:16
Alignment explanation
Indices: 5215159--5215193 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
5215149 GAAAAAAAGG
5215159 GAAAATAAATAAAAAAA
1 GAAAATAAA-AAAAAAA
5215176 GAAAATAAAAAAAGAAA
1 GAAAATAAAAAAA-AAA
5215193 G
1 G
5215194 GGAAACAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (16 bp):
GAAAATAAAAAAAAAA
Found at i:5215185 original size:12 final size:13
Alignment explanation
Indices: 5215165--5215192 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5215155 AAGGGAAAAT
5215165 AAATAAAAAAAGA
1 AAATAAAAAAAGA
5215178 AAATAAAAAAAGA
1 AAATAAAAAAAGA
5215191 AA
1 AA
5215193 GGGAAACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.86, C:0.00, G:0.07, T:0.07
Consensus pattern (13 bp):
AAATAAAAAAAGA
Found at i:5228996 original size:27 final size:27
Alignment explanation
Indices: 5228958--5229013 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
5228948 AAACTAGACC
5228958 CAATAAAATATATGATGGAATCACCTA
1 CAATAAAATATATGATGGAATCACCTA
*
5228985 CAATAAAGTATATGATGGAATCACCTA
1 CAATAAAATATATGATGGAATCACCTA
5229012 CA
1 CA
5229014 CTTTCAGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.25
Consensus pattern (27 bp):
CAATAAAATATATGATGGAATCACCTA
Found at i:5232052 original size:77 final size:77
Alignment explanation
Indices: 5231843--5232360 Score: 718
Period size: 76 Copynumber: 6.7 Consensus size: 77
5231833 TTTCAAAAAA
* *
5231843 ATCAACTCATAATCCAAGAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTTTTTCAATTTC
1 ATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAGGTATTTTTTCAATTTC
*
5231908 TTTTTTTTTCAAAG
66 --TATTTTTCAAAG
* * * * *
5231922 ATCAACTCATAATTCGAGAGGTGAGTTGAGCTTCAGGTCACACGTCGAGGTATTTTTTCAATTTC
1 ATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAGGTATTTTTTCAATTTC
*
5231987 TTTTTTTCAAAG
66 TATTTTTCAAAG
* * *
5231999 ATCAACTCATAATCCAAGAGGTGAGTTGAGCCTCGAGTCGCACGCCGAAGTATTTTTTCAATTTC
1 ATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAGGTATTTTTTCAATTTC
*
5232064 TGTTTTTCAAAG
66 TATTTTTCAAAG
* **
5232076 ATCAACTCATAATCTGAGAGGTGAGTTGAGCCTCGGGTTACACGCCGAGGTA-TTTTTCAATTTC
1 ATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAGGTATTTTTTCAATTTC
5232140 TATTTTTCAAAG
66 TATTTTTCAAAG
* * * * *
5232152 ATCAACTTATAATTCGAGAGGTGAGTTGAGTCTTGGGTCGCACGCCGAGGTA-TTTTTCAATCTC
1 ATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAGGTATTTTTTCAATTTC
5232216 TATTTTTCAAAG
66 TATTTTTCAAAG
* * *
5232228 GTCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAAGCA-TTTTTCAATTTC
1 ATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAGGTATTTTTTCAATTTC
*
5232292 TGTTTTTCAAAG
66 TATTTTTCAAAG
* * * * * *
5232304 ATCAACTCATAATCCGATAAGTGACTTGAGCCTCGGGTTGCATGCCAAGGTATTTTT
1 ATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAGGTATTTTT
5232361 AAATTTCAGT
Statistics
Matches: 391, Mismatches: 47, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
76 201 0.51
77 130 0.33
79 60 0.15
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (77 bp):
ATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAGGTATTTTTTCAATTTC
TATTTTTCAAAG
Found at i:5232926 original size:29 final size:30
Alignment explanation
Indices: 5232888--5232988 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 30
5232878 AAAATTTACT
* *
5232888 AATTATATTTTG-GCTCTAACTTTTTCTAA
1 AATTACATTTTGACCTCTAACTTTTTCTAA
* * *
5232917 AATTACATTTTGCCCCCTAACTTTTCCTAA
1 AATTACATTTTGACCTCTAACTTTTTCTAA
*
5232947 AATTATATTTTGACCTCTAAC-TTTTCTTAA
1 AATTACATTTTGACCTCTAACTTTTTC-TAA
5232977 AATTACATTTTG
1 AATTACATTTTG
5232989 GCCCCGTGAG
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
29 15 0.25
30 46 0.75
ACGTcount: A:0.29, C:0.19, G:0.05, T:0.48
Consensus pattern (30 bp):
AATTACATTTTGACCTCTAACTTTTTCTAA
Found at i:5233711 original size:6 final size:6
Alignment explanation
Indices: 5233700--5233787 Score: 108
Period size: 6 Copynumber: 14.8 Consensus size: 6
5233690 AGGGTTAGAG
** * * *
5233700 AGAAAA AG-AAA AGAGGA GGAAAA AGAAAC A-AAAA AGAAAA GAAAAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA -AGAAAA
5233747 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAA
5233788 GGGAAACAGT
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
5 9 0.13
6 55 0.80
7 5 0.07
ACGTcount: A:0.80, C:0.01, G:0.19, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:5237917 original size:10 final size:9
Alignment explanation
Indices: 5237871--5238023 Score: 51
Period size: 10 Copynumber: 15.4 Consensus size: 9
5237861 ACATTAACCC
*
5237871 TAATTATTA
1 TAATTTTTA
5237880 TAATTTTTTTA
1 TAA--TTTTTA
*
5237891 TAATATTTA
1 TAATTTTTA
5237900 TAAGTTTTTA
1 TAA-TTTTTA
5237910 TGAATTTTTTTTA
1 T-AA---TTTTTA
5237923 TAA-TTTTA
1 TAATTTTTA
*
5237931 TAAGTTTATA
1 TAA-TTTTTA
* *
5237941 GAAAGTTTTA
1 -TAATTTTTA
5237951 -AATATTTTAA
1 TAAT-TTTT-A
*
5237961 TACACTTTTA
1 TA-ATTTTTA
*
5237971 T-TTTTTTA
1 TAATTTTTA
*
5237979 GAATTTATTA
1 TAATTT-TTA
5237989 TAATTTTTA
1 TAATTTTTA
*
5237998 TAAACTTTTA
1 T-AATTTTTA
5238008 TGAAATTTTTAA
1 T--AATTTTT-A
5238020 TAAT
1 TAAT
5238024 ATTTNNNNNN
Statistics
Matches: 109, Mismatches: 17, Indels: 35
0.68 0.11 0.22
Matches are distributed among these distances:
8 15 0.14
9 22 0.20
10 36 0.33
11 24 0.22
12 5 0.05
13 7 0.06
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.58
Consensus pattern (9 bp):
TAATTTTTA
Found at i:5237919 original size:31 final size:30
Alignment explanation
Indices: 5237877--5237937 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 30
5237867 ACCCTAATTA
5237877 TTATAA-TTTTTTTATAATATTTATAAGTTT
1 TTATAATTTTTTTTATAAT-TTTATAAGTTT
5237907 TTATGAATTTTTTTTATAATTTTATAAGTTT
1 TTAT-AATTTTTTTTATAATTTTATAAGTTT
5237938 ATAGAAAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 4 0.14
31 13 0.45
32 12 0.41
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (30 bp):
TTATAATTTTTTTTATAATTTTATAAGTTT
Found at i:5237949 original size:29 final size:32
Alignment explanation
Indices: 5237885--5237957 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 32
5237875 TATTATAATT
* **
5237885 TTTTTATAATATTTATAAGTTTTTATGAATTT
1 TTTTTATAATATTTATAAGTTTATATGAATAG
5237917 TTTTTATAAT-TTTATAAGTTTATA-GAA-AG
1 TTTTTATAATATTTATAAGTTTATATGAATAG
5237946 -TTTTA-AATATTT
1 TTTTTATAATATTT
5237958 TAATACACTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
27 3 0.08
28 8 0.22
30 3 0.08
31 13 0.35
32 10 0.27
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (32 bp):
TTTTTATAATATTTATAAGTTTATATGAATAG
Found at i:5240257 original size:1 final size:1
Alignment explanation
Indices: 5240253--5240299 Score: 94
Period size: 1 Copynumber: 47.0 Consensus size: 1
5240243 TTTTCTTATC
5240253 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5240300 GTAATAAATC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5243303 original size:8 final size:8
Alignment explanation
Indices: 5243286--5243325 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
5243276 TCATCCCATC
5243286 AAAAATTTT
1 AAAAA-TTT
5243295 AAAAATTT
1 AAAAATTT
*
5243303 AAAAATAT
1 AAAAATTT
*
5243311 AAAAATAT
1 AAAAATTT
5243319 AAAAATT
1 AAAAATT
5243326 ATTTTGAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
8 24 0.83
9 5 0.17
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AAAAATTT
Found at i:5246535 original size:30 final size:29
Alignment explanation
Indices: 5246502--5246557 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
5246492 AAAGGCCATT
5246502 TTTTTTCAA-AATTTACCGAAATGGGCCGG
1 TTTTTT-AATAATTTACCGAAATGGGCCGG
* *
5246531 TTTTTTAATTATTTACCGGAATGGGCC
1 TTTTTTAATAATTTACCGAAATGGGCC
5246558 ATTTTCCGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (29 bp):
TTTTTTAATAATTTACCGAAATGGGCCGG
Found at i:5255534 original size:14 final size:14
Alignment explanation
Indices: 5255512--5255555 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
5255502 CTAAATCTTG
*
5255512 AACTCTGAACCTCA
1 AACTATGAACCTCA
* *
5255526 AACTTTGAACCTAA
1 AACTATGAACCTCA
*
5255540 AACTATAAACCTCA
1 AACTATGAACCTCA
5255554 AA
1 AA
5255556 TCATGAACAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.45, C:0.27, G:0.05, T:0.23
Consensus pattern (14 bp):
AACTATGAACCTCA
Found at i:5255687 original size:29 final size:29
Alignment explanation
Indices: 5255650--5255707 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
5255640 AAGTTTATAC
5255650 AATACGAACAAGAATTAATTAAAATTTAT
1 AATACGAACAAGAATTAATTAAAATTTAT
5255679 AATACGAACAAGAATTAATTAAAATTTAT
1 AATACGAACAAGAATTAATTAAAATTTAT
5255708 CTAAAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.31
Consensus pattern (29 bp):
AATACGAACAAGAATTAATTAAAATTTAT
Found at i:5256198 original size:12 final size:12
Alignment explanation
Indices: 5256183--5256217 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
5256173 TTTTTACTTA
5256183 AATTTTTTTTAT
1 AATTTTTTTTAT
5256195 AATTTTTGTTTAT
1 AATTTTT-TTTAT
*
5256208 GATTTTTTTT
1 AATTTTTTTT
5256218 GAACCTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.74
Consensus pattern (12 bp):
AATTTTTTTTAT
Found at i:5258355 original size:14 final size:14
Alignment explanation
Indices: 5258333--5258376 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
5258323 CTAAATCTTG
*
5258333 AACTCTGAACCTCA
1 AACTATGAACCTCA
* *
5258347 AACTTTGAACCTAA
1 AACTATGAACCTCA
*
5258361 AACTATAAACCTCA
1 AACTATGAACCTCA
5258375 AA
1 AA
5258377 TCATGAACAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.45, C:0.27, G:0.05, T:0.23
Consensus pattern (14 bp):
AACTATGAACCTCA
Found at i:5258691 original size:7 final size:7
Alignment explanation
Indices: 5258679--5258711 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
5258669 GTTATACACA
5258679 TATAAGG
1 TATAAGG
5258686 TATAAGG
1 TATAAGG
5258693 TATAAGG
1 TATAAGG
5258700 TATAAGG
1 TATAAGG
5258707 TATAA
1 TATAA
5258712 TATTATGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.45, C:0.00, G:0.24, T:0.30
Consensus pattern (7 bp):
TATAAGG
Found at i:5259912 original size:16 final size:16
Alignment explanation
Indices: 5259891--5259922 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5259881 TAATAATTTC
*
5259891 TAAAAACATGTATATG
1 TAAAAAAATGTATATG
5259907 TAAAAAAATGTATATG
1 TAAAAAAATGTATATG
5259923 AATTAGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.03, G:0.12, T:0.31
Consensus pattern (16 bp):
TAAAAAAATGTATATG
Found at i:5260209 original size:3 final size:3
Alignment explanation
Indices: 5260201--5260234 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
5260191 ATAGGCGTAT
* *
5260201 ATA ATA ATA ATA ATA ATA TTA ATA ATA ACA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5260235 ATAGGATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5260531 original size:14 final size:14
Alignment explanation
Indices: 5260509--5260552 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
5260499 CTAAATCTTG
*
5260509 AACTCTGAACCTCA
1 AACTATGAACCTCA
* *
5260523 AACTTTGAACCTAA
1 AACTATGAACCTCA
*
5260537 AACTATAAACCTCA
1 AACTATGAACCTCA
5260551 AA
1 AA
5260553 TCATGAACAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.45, C:0.27, G:0.05, T:0.23
Consensus pattern (14 bp):
AACTATGAACCTCA
Found at i:5260684 original size:29 final size:29
Alignment explanation
Indices: 5260647--5260704 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
5260637 AAGTTTATAC
5260647 AATACGAACAAGAATTAATTAAAATTTAT
1 AATACGAACAAGAATTAATTAAAATTTAT
5260676 AATACGAACAAGAATTAATTAAAATTTAT
1 AATACGAACAAGAATTAATTAAAATTTAT
5260705 CTAAAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.31
Consensus pattern (29 bp):
AATACGAACAAGAATTAATTAAAATTTAT
Found at i:5261232 original size:16 final size:16
Alignment explanation
Indices: 5261211--5261241 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5261201 ATATTATGAA
5261211 AAAAATAAAAATATTC
1 AAAAATAAAAATATTC
*
5261227 AAAAATACAAATATT
1 AAAAATAAAAATATT
5261242 TTTTCTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAATAAAAATATTC
Found at i:5261410 original size:12 final size:12
Alignment explanation
Indices: 5261395--5261429 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
5261385 TTTTTACTTA
5261395 AATTTTTTTTAT
1 AATTTTTTTTAT
5261407 AATTTTTGTTTAT
1 AATTTTT-TTTAT
*
5261420 GATTTTTTTT
1 AATTTTTTTT
5261430 GAACCTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.74
Consensus pattern (12 bp):
AATTTTTTTTAT
Found at i:5263568 original size:14 final size:14
Alignment explanation
Indices: 5263546--5263589 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
5263536 CTAAATCTTG
*
5263546 AACTCTGAACCTCA
1 AACTATGAACCTCA
* *
5263560 AACTTTGAACCTAA
1 AACTATGAACCTCA
*
5263574 AACTATAAACCTCA
1 AACTATGAACCTCA
5263588 AA
1 AA
5263590 TCATGAACAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.45, C:0.27, G:0.05, T:0.23
Consensus pattern (14 bp):
AACTATGAACCTCA
Found at i:5263904 original size:7 final size:7
Alignment explanation
Indices: 5263892--5263924 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
5263882 GTTATACACA
5263892 TATAAGG
1 TATAAGG
5263899 TATAAGG
1 TATAAGG
5263906 TATAAGG
1 TATAAGG
5263913 TATAAGG
1 TATAAGG
5263920 TATAA
1 TATAA
5263925 TATTATGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.45, C:0.00, G:0.24, T:0.30
Consensus pattern (7 bp):
TATAAGG
Found at i:5265183 original size:13 final size:14
Alignment explanation
Indices: 5265161--5265191 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
5265151 AGTATATATA
5265161 AAAAAGTAAAAAAC
1 AAAAAGTAAAAAAC
5265175 AAAAA-TAAAAAAC
1 AAAAAGTAAAAAAC
5265188 AAAA
1 AAAA
5265192 CATATGTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.84, C:0.06, G:0.03, T:0.06
Consensus pattern (14 bp):
AAAAAGTAAAAAAC
Found at i:5265969 original size:5 final size:5
Alignment explanation
Indices: 5265961--5265994 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
5265951 TCGTTATTTT
*
5265961 AAATA AAATA AAATGA AAATA AAAGA AAATA AAA
1 AAATA AAATA AAAT-A AAATA AAATA AAATA AAA
5265995 AAATATGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (5 bp):
AAATA
Found at i:5265995 original size:16 final size:16
Alignment explanation
Indices: 5265961--5265995 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5265951 TCGTTATTTT
* *
5265961 AAATAAAATAAAATGA
1 AAATAAAAGAAAATAA
5265977 AAATAAAAGAAAATAA
1 AAATAAAAGAAAATAA
5265993 AAA
1 AAA
5265996 AATATGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (16 bp):
AAATAAAAGAAAATAA
Found at i:5266006 original size:26 final size:26
Alignment explanation
Indices: 5265961--5266010 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
5265951 TCGTTATTTT
5265961 AAATAAAATAAAATGAAAATAAAAGA
1 AAATAAAATAAAATGAAAATAAAAGA
*
5265987 AAATAAAA-AAATATGGAAATAAAA
1 AAATAAAATAAA-ATGAAAATAAAA
5266011 ACAATAGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (26 bp):
AAATAAAATAAAATGAAAATAAAAGA
Found at i:5266900 original size:170 final size:171
Alignment explanation
Indices: 5266711--5267053 Score: 679
Period size: 170 Copynumber: 2.0 Consensus size: 171
5266701 TCGCTCAATA
5266711 AAAAATTAAAATTTAACTTAATTGTATTTAAAAAATGAATTTTTATTTTTTACTTAAATTTTTTT
1 AAAAATTAAAATTTAACTTAATTGTATTTAAAAAATGAATTTTTATTTTTTACTTAAATTTTTTT
5266776 ATAATTTTTGTTTATGATTTTTTTTGAACCTTTCAAAATTTGAATAAGACTGTATTGAGAACTAA
66 ATAATTTTTGTTTATGATTTTTTTTGAACCTTTCAAAATTTGAATAAGACTGTATTGAGAACTAA
5266841 ATGTACATTTTGAATTACTTACCCTTCCTTATCAAATAGTG
131 ATGTACATTTTGAATTACTTACCCTTCCTTATCAAATAGTG
5266882 AAAAATTAAAA-TTAACTTAATTGTATTTAAAAAATGAATTTTTATTTTTTACTTAAATTTTTTT
1 AAAAATTAAAATTTAACTTAATTGTATTTAAAAAATGAATTTTTATTTTTTACTTAAATTTTTTT
5266946 ATAATTTTTGTTTATGATTTTTTTTGAACCTTTCAAAATTTGAATAAGACTGTATTGAGAACTAA
66 ATAATTTTTGTTTATGATTTTTTTTGAACCTTTCAAAATTTGAATAAGACTGTATTGAGAACTAA
5267011 ATGTACATTTTGAATTACTTACCCTTCCTTATCAAATAGTG
131 ATGTACATTTTGAATTACTTACCCTTCCTTATCAAATAGTG
5267052 AA
1 AA
5267054 GTATTTATAG
Statistics
Matches: 172, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
170 161 0.94
171 11 0.06
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.47
Consensus pattern (171 bp):
AAAAATTAAAATTTAACTTAATTGTATTTAAAAAATGAATTTTTATTTTTTACTTAAATTTTTTT
ATAATTTTTGTTTATGATTTTTTTTGAACCTTTCAAAATTTGAATAAGACTGTATTGAGAACTAA
ATGTACATTTTGAATTACTTACCCTTCCTTATCAAATAGTG
Found at i:5267146 original size:15 final size:15
Alignment explanation
Indices: 5267128--5267158 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5267118 CAAACTACCT
5267128 GCTAATAGACTAACA
1 GCTAATAGACTAACA
5267143 GCTAATAGACTAACA
1 GCTAATAGACTAACA
5267158 G
1 G
5267159 AATTTAGGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.19, G:0.16, T:0.19
Consensus pattern (15 bp):
GCTAATAGACTAACA
Found at i:5272516 original size:16 final size:16
Alignment explanation
Indices: 5272495--5272530 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
5272485 AAACAAATTA
*
5272495 ATATAAGCAAATATTT
1 ATATAAACAAATATTT
5272511 ATATAAACAAATATTT
1 ATATAAACAAATATTT
5272527 ATAT
1 ATAT
5272531 TTATGTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.39
Consensus pattern (16 bp):
ATATAAACAAATATTT
Found at i:5275957 original size:31 final size:31
Alignment explanation
Indices: 5275900--5275958 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
5275890 AACAACTCAT
*
5275900 TGACTTAAATAAAAGCTTTTGAATAGTTCAG
1 TGACTTAAATAAAAGCTTTAGAATAGTTCAG
5275931 TGACTTAAATGAAAA-CTTTCAG-ATAGTT
1 TGACTTAAAT-AAAAGCTTT-AGAATAGTT
5275959 AAATGATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (31 bp):
TGACTTAAATAAAAGCTTTAGAATAGTTCAG
Found at i:5279711 original size:19 final size:18
Alignment explanation
Indices: 5279684--5279722 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
5279674 ATTAAAATTT
*
5279684 TAAAAATCAAAATTTAAAC
1 TAAAAATC-AAATTCAAAC
*
5279703 TAAAGATCAAATTCAAAC
1 TAAAAATCAAATTCAAAC
5279721 TA
1 TA
5279723 TTTATACGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.59, C:0.13, G:0.03, T:0.26
Consensus pattern (18 bp):
TAAAAATCAAATTCAAAC
Found at i:5281405 original size:16 final size:16
Alignment explanation
Indices: 5281384--5281422 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
5281374 TTATGTGTAT
5281384 GGTAAG-CAAATAATAA
1 GGTAAGTCAAAT-ATAA
*
5281400 GGTAAGTGAAATATAA
1 GGTAAGTCAAATATAA
5281416 GGTAAGT
1 GGTAAGT
5281423 ATTATTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.49, C:0.03, G:0.26, T:0.23
Consensus pattern (16 bp):
GGTAAGTCAAATATAA
Found at i:5281532 original size:36 final size:38
Alignment explanation
Indices: 5281494--5281572 Score: 101
Period size: 36 Copynumber: 2.1 Consensus size: 38
5281484 ATATTGACTT
* *
5281494 GAAAATGGAAAAGT-AAATTTGAATTGAATTGTG-A-TT
1 GAAAATGAAAAAGTGAAA-TTGAATTGAAATGTGAATTT
*
5281530 GAAAGTGAAAAAGTGAAATTGAATTGAAATGTGAATTT
1 GAAAATGAAAAAGTGAAATTGAATTGAAATGTGAATTT
5281568 GAAAA
1 GAAAA
5281573 GTATGTGTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
36 26 0.72
37 4 0.11
38 6 0.17
ACGTcount: A:0.48, C:0.00, G:0.23, T:0.29
Consensus pattern (38 bp):
GAAAATGAAAAAGTGAAATTGAATTGAAATGTGAATTT
Found at i:5281822 original size:20 final size:22
Alignment explanation
Indices: 5281766--5281828 Score: 94
Period size: 23 Copynumber: 2.9 Consensus size: 22
5281756 CTTTGCCTAC
5281766 CAGGCACTTTATGTGTCGTACAT
1 CAGGCACTTTATGTGTCGTA-AT
*
5281789 CAGGCACTTTATGTGTCGT-TT
1 CAGGCACTTTATGTGTCGTAAT
5281810 CAGGCAC-TTATGTGTCGTA
1 CAGGCACTTTATGTGTCGTA
5281829 TACTGATTAG
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
20 11 0.29
21 8 0.21
23 19 0.50
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.37
Consensus pattern (22 bp):
CAGGCACTTTATGTGTCGTAAT
Found at i:5283888 original size:17 final size:17
Alignment explanation
Indices: 5283866--5283900 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5283856 AAATACATAG
5283866 ATAAATACTA-TAATAAT
1 ATAAATA-TAGTAATAAT
5283883 ATAAATATAGTAATAAT
1 ATAAATATAGTAATAAT
5283900 A
1 A
5283901 AGAATATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (17 bp):
ATAAATATAGTAATAAT
Found at i:5296995 original size:16 final size:16
Alignment explanation
Indices: 5296974--5297004 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5296964 ATAACTAATC
5296974 GGTATTAATCATTCCG
1 GGTATTAATCATTCCG
5296990 GGTATTAATCATTCC
1 GGTATTAATCATTCC
5297005 AGTTTTGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (16 bp):
GGTATTAATCATTCCG
Found at i:5297203 original size:41 final size:41
Alignment explanation
Indices: 5297147--5297229 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
5297137 AAAAAAGAAT
5297147 GAATCAAACAATCCCAGTTAGAAGAAGATAGGTATAACCCA
1 GAATCAAACAATCCCAGTTAGAAGAAGATAGGTATAACCCA
*
5297188 GAATCAAACAATCCCAGTTAGAAGATGATAGGTATAACCCA
1 GAATCAAACAATCCCAGTTAGAAGAAGATAGGTATAACCCA
5297229 G
1 G
5297230 CTAAGCTTCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.45, C:0.19, G:0.18, T:0.18
Consensus pattern (41 bp):
GAATCAAACAATCCCAGTTAGAAGAAGATAGGTATAACCCA
Found at i:5302555 original size:14 final size:14
Alignment explanation
Indices: 5302536--5302566 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
5302526 TATTTATTGT
5302536 TATTTGAAGAATAA
1 TATTTGAAGAATAA
5302550 TATTTGAAGAATAA
1 TATTTGAAGAATAA
5302564 TAT
1 TAT
5302567 GGAATACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (14 bp):
TATTTGAAGAATAA
Found at i:5305930 original size:18 final size:18
Alignment explanation
Indices: 5305909--5305946 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
5305899 TAAAAAAATA
5305909 TATAAAT-TTTAGAATTTT
1 TATAAATATTTAG-ATTTT
*
5305927 TATAAATATTTTGATTTT
1 TATAAATATTTAGATTTT
5305945 TA
1 TA
5305947 ATTTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (18 bp):
TATAAATATTTAGATTTT
Found at i:5311914 original size:21 final size:21
Alignment explanation
Indices: 5311890--5311929 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5311880 AGTTTGATAA
5311890 ATTGAAATTTT-AAAATTAATT
1 ATTG-AATTTTCAAAATTAATT
*
5311911 ATTGAATTTTCAATATTAA
1 ATTGAATTTTCAAAATTAA
5311930 ATTTGATGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (21 bp):
ATTGAATTTTCAAAATTAATT
Found at i:5312950 original size:24 final size:24
Alignment explanation
Indices: 5312916--5312961 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5312906 TATATGAAAT
* *
5312916 ATAAATTTTAAATATTTTTAAGTA
1 ATAAATATTAAATATTTATAAGTA
*
5312940 ATAAATATTAATTATTTATAAG
1 ATAAATATTAAATATTTATAAG
5312962 ATTTAATTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
ATAAATATTAAATATTTATAAGTA
Found at i:5317184 original size:20 final size:21
Alignment explanation
Indices: 5317159--5317214 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
5317149 ATGCCCTAGG
5317159 ATGCACTTCATGTGCCA-GAT
1 ATGCACTTCATGTGCCAGGAT
* **
5317179 ATGCACTACATGCACCAGGAT
1 ATGCACTTCATGTGCCAGGAT
5317200 A--CACTTCATGTGCCA
1 ATGCACTTCATGTGCCA
5317215 AGATGTACTA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 11 0.38
20 14 0.48
21 4 0.14
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.25
Consensus pattern (21 bp):
ATGCACTTCATGTGCCAGGAT
Found at i:5317247 original size:17 final size:19
Alignment explanation
Indices: 5317208--5317247 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
5317198 ATACACTTCA
5317208 TGTGCCAAGATGTACTATG
1 TGTGCCAAGATGTACTATG
*
5317227 TGTGCC-AGTATGTACTTTG
1 TGTGCCAAG-ATGTACTATG
5317246 TG
1 TG
5317248 CACTAGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.20, C:0.15, G:0.28, T:0.38
Consensus pattern (19 bp):
TGTGCCAAGATGTACTATG
Found at i:5319041 original size:19 final size:20
Alignment explanation
Indices: 5319017--5319066 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 20
5319007 ATGTTAGATA
*
5319017 ATTAATTAAG-AAAAGTATG
1 ATTAATTAAGAAAAAATATG
5319036 ATTAATTAAGATAAAAATATG
1 ATTAATTAAGA-AAAAATATG
5319057 ATTAATTAAG
1 ATTAATTAAG
5319067 TTTAATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 10 0.36
21 18 0.64
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.34
Consensus pattern (20 bp):
ATTAATTAAGAAAAAATATG
Found at i:5321895 original size:12 final size:12
Alignment explanation
Indices: 5321866--5321898 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
5321856 TTTTAAATGA
*
5321866 TATTTATTATTT
1 TATTTAGTATTT
5321878 TA-TTAGTATTT
1 TATTTAGTATTT
5321889 TATTTAGTAT
1 TATTTAGTAT
5321899 ATATAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (12 bp):
TATTTAGTATTT
Found at i:5325493 original size:36 final size:35
Alignment explanation
Indices: 5325431--5325498 Score: 91
Period size: 36 Copynumber: 1.9 Consensus size: 35
5325421 ATTTTCAGTG
* *
5325431 AGTTTTAAAGAGTTTTTATGATAATAATATTCTCTT
1 AGTTTTAAAGAGTTTGTATGAGAATAAT-TTCTCTT
* *
5325467 AGTTTTAAAGAGTTTGTGTGGGAATAATTTCT
1 AGTTTTAAAGAGTTTGTATGAGAATAATTTCT
5325499 ACTTTTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 4 0.14
36 24 0.86
ACGTcount: A:0.31, C:0.04, G:0.18, T:0.47
Consensus pattern (35 bp):
AGTTTTAAAGAGTTTGTATGAGAATAATTTCTCTT
Found at i:5326803 original size:2 final size:2
Alignment explanation
Indices: 5326796--5326820 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5326786 TGATAACACC
5326796 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5326821 GTCTCTTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5328355 original size:6 final size:6
Alignment explanation
Indices: 5328344--5328377 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
5328334 TTGGTGTAGC
*
5328344 GACAGG GACAGG GGCAGG GACAGG GACAGG GACA
1 GACAGG GACAGG GACAGG GACAGG GACAGG GACA
5328378 AAGCAACATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.32, C:0.18, G:0.50, T:0.00
Consensus pattern (6 bp):
GACAGG
Found at i:5332079 original size:17 final size:18
Alignment explanation
Indices: 5332053--5332093 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
5332043 TTCAATTAAG
*
5332053 TTAA-TTTTAAAGTT-TT
1 TTAATTTTTAAAATTATT
5332069 TTAATTTTTAAAATTATT
1 TTAATTTTTAAAATTATT
5332087 TT-ATTTT
1 TTAATTTT
5332094 GTTGATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 4 0.18
17 14 0.64
18 4 0.18
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (18 bp):
TTAATTTTTAAAATTATT
Found at i:5336336 original size:31 final size:31
Alignment explanation
Indices: 5336299--5336357 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
5336289 AACGATCACT
5336299 AACTATTCAAAAGTTTTCATTTAAGTCATTA
1 AACTATTCAAAAGTTTTCATTTAAGTCATTA
** *
5336330 AACTATTTGAAAGTTTTTATTTAAGTCA
1 AACTATTCAAAAGTTTTCATTTAAGTCA
5336358 CTAGGCTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.44
Consensus pattern (31 bp):
AACTATTCAAAAGTTTTCATTTAAGTCATTA
Found at i:5348076 original size:79 final size:80
Alignment explanation
Indices: 5347969--5348129 Score: 315
Period size: 79 Copynumber: 2.0 Consensus size: 80
5347959 TTTATAAAAT
5347969 AATATTAATATAATATTAAACTCATATATAATAAAAATTAAGCCTAAAAATCGAATCCAATATGA
1 AATATTAATATAATATTAAACTCATATATAATAAAAATTAAGCCTAAAAATCGAATCCAATATGA
5348034 TTTAAACTCGAATTA
66 TTTAAACTCGAATTA
5348049 AATATTAATAT-ATATTAAACTCATATATAATAAAAATTAAGCCTAAAAATCGAATCCAATATGA
1 AATATTAATATAATATTAAACTCATATATAATAAAAATTAAGCCTAAAAATCGAATCCAATATGA
5348113 TTTAAACTCGAATTA
66 TTTAAACTCGAATTA
5348128 AA
1 AA
5348130 AGCTCGAAAC
Statistics
Matches: 81, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
79 70 0.86
80 11 0.14
ACGTcount: A:0.52, C:0.11, G:0.05, T:0.32
Consensus pattern (80 bp):
AATATTAATATAATATTAAACTCATATATAATAAAAATTAAGCCTAAAAATCGAATCCAATATGA
TTTAAACTCGAATTA
Found at i:5348655 original size:30 final size:30
Alignment explanation
Indices: 5348614--5348676 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
5348604 TCAATAATTT
*
5348614 AATTGATTGTTTATATTAGATT-AAAGACTC
1 AATTAATTGTTTATATTAGATTAAAAG-CTC
*
5348644 AATTAATTGTTTATATTCGATTAAAAGCTC
1 AATTAATTGTTTATATTAGATTAAAAGCTC
5348674 AAT
1 AAT
5348677 CGATGATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 26 0.87
31 4 0.13
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (30 bp):
AATTAATTGTTTATATTAGATTAAAAGCTC
Found at i:5349056 original size:14 final size:16
Alignment explanation
Indices: 5349033--5349072 Score: 57
Period size: 14 Copynumber: 2.6 Consensus size: 16
5349023 GTTTCCAAAA
5349033 TTTATTTTTTCTCT-C
1 TTTATTTTTTCTCTCC
*
5349048 TTT-TTTTTTCTTTCC
1 TTTATTTTTTCTCTCC
5349063 TTTATTTTTT
1 TTTATTTTTT
5349073 TCCACCAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 9 0.41
15 7 0.32
16 6 0.27
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTATTTTTTCTCTCC
Found at i:5357035 original size:50 final size:50
Alignment explanation
Indices: 5356981--5357112 Score: 151
Period size: 50 Copynumber: 2.6 Consensus size: 50
5356971 CATTTAGGTT
* * * *
5356981 ATGAGAGGCCCCATGTAAGACCACGTCTGGGACTTGGCGTTGGCACCGAG
1 ATGAGAGGCCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAG
* *
5357031 ATGAGAGGTCCCC-CGTAAGACCATGTCTGGGACATGGCATGGGCACCGAT
1 ATGAGAGG-CCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAG
** *
5357081 ATGA-AAACTCCCATGTAAGACCATATCTGGGA
1 ATGAGAGGC-CCCATGTAAGACCATGTCTGGGA
5357113 TATGACATTG
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
48 1 0.01
49 4 0.06
50 60 0.87
51 4 0.06
ACGTcount: A:0.27, C:0.25, G:0.30, T:0.19
Consensus pattern (50 bp):
ATGAGAGGCCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAG
Found at i:5377116 original size:7 final size:7
Alignment explanation
Indices: 5377104--5377135 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
5377094 CTTTCATATT
5377104 TTCTTTG
1 TTCTTTG
5377111 TTCTTTG
1 TTCTTTG
5377118 TTCTTTG
1 TTCTTTG
*
5377125 TTCTTTA
1 TTCTTTG
5377132 TTCT
1 TTCT
5377136 CTTCATCTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.03, C:0.16, G:0.09, T:0.72
Consensus pattern (7 bp):
TTCTTTG
Found at i:5377259 original size:14 final size:14
Alignment explanation
Indices: 5377240--5377267 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5377230 GAGCATTAAT
5377240 TTAAAGAGATTTTA
1 TTAAAGAGATTTTA
5377254 TTAAAGAGATTTTA
1 TTAAAGAGATTTTA
5377268 ATTTTCCAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (14 bp):
TTAAAGAGATTTTA
Found at i:5377371 original size:11 final size:11
Alignment explanation
Indices: 5377355--5377384 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
5377345 ATACTATCAA
5377355 TTTCTCTTCTT
1 TTTCTCTTCTT
5377366 TTTCTC-TCTT
1 TTTCTCTTCTT
5377376 TTTCTCTTC
1 TTTCTCTTC
5377385 CTCCCTCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTCTCTTCTT
Found at i:5380312 original size:18 final size:19
Alignment explanation
Indices: 5380289--5380338 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
5380279 GAGTTAAACT
*
5380289 CACCACCGCCGCC-GCCGC
1 CACCACCGCCGCCAACCGC
*
5380307 CACCACCACC-CCAACCGC
1 CACCACCGCCGCCAACCGC
*
5380325 CACCACTGCCGCCA
1 CACCACCGCCGCCA
5380339 CTGATACCGC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 2 0.08
18 21 0.81
19 3 0.12
ACGTcount: A:0.20, C:0.64, G:0.14, T:0.02
Consensus pattern (19 bp):
CACCACCGCCGCCAACCGC
Found at i:5388235 original size:17 final size:17
Alignment explanation
Indices: 5388205--5388238 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5388195 AAAAAGTTAT
* *
5388205 TAAATTTTATAAAAAAA
1 TAAATGTTAGAAAAAAA
5388222 TAAATGTTAGAAAAAAA
1 TAAATGTTAGAAAAAAA
5388239 AATTATAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (17 bp):
TAAATGTTAGAAAAAAA
Found at i:5388319 original size:30 final size:30
Alignment explanation
Indices: 5388262--5388319 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
5388252 GTAAAAGAAA
* **
5388262 ATAAAAAAATTGCAAAATTTATAAAAAATC
1 ATAAAAAAATTACAAAATGCATAAAAAATC
* *
5388292 ATAAAAAAATTATAAAATGCATCAAAAA
1 ATAAAAAAATTACAAAATGCATAAAAAA
5388320 GACCTACAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.66, C:0.07, G:0.03, T:0.24
Consensus pattern (30 bp):
ATAAAAAAATTACAAAATGCATAAAAAATC
Found at i:5388526 original size:11 final size:10
Alignment explanation
Indices: 5388491--5388575 Score: 52
Period size: 10 Copynumber: 8.4 Consensus size: 10
5388481 GGTATGATAC
5388491 TTTTTATAAT
1 TTTTTATAAT
*
5388501 TTTTTTTACGA-
1 TTTTTATA--AT
5388512 TTTTTATAACT
1 TTTTTATAA-T
*
5388523 TTTTTCTAA-
1 TTTTTATAAT
5388532 TTTTTA-AAT
1 TTTTTATAAT
5388541 ATTTTTAT-AT
1 -TTTTTATAAT
*
5388551 TTTTTACTAAA
1 TTTTTA-TAAT
* *
5388562 ATTTAATAAT
1 TTTTTATAAT
5388572 TTTT
1 TTTT
5388576 AGATTGTAAC
Statistics
Matches: 57, Mismatches: 9, Indels: 18
0.68 0.11 0.21
Matches are distributed among these distances:
8 2 0.04
9 12 0.21
10 22 0.39
11 20 0.35
12 1 0.02
ACGTcount: A:0.29, C:0.05, G:0.01, T:0.65
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:5388536 original size:21 final size:20
Alignment explanation
Indices: 5388491--5388546 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
5388481 GGTATGATAC
*
5388491 TTTTTATAATTTTTTTTACGA
1 TTTTTATAATTTTTTCTAC-A
5388512 TTTTTATAACTTTTTTCTA-A
1 TTTTTATAA-TTTTTTCTACA
5388532 TTTTTA-AATATTTTT
1 TTTTTATAAT-TTTTT
5388547 ATATTTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 1 0.03
19 7 0.22
20 7 0.22
21 9 0.28
22 8 0.25
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (20 bp):
TTTTTATAATTTTTTCTACA
Found at i:5388566 original size:29 final size:30
Alignment explanation
Indices: 5388511--5388576 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 30
5388501 TTTTTTTACG
**
5388511 ATTTTTATAACTTTTTTCTAATTTTTAA-A
1 ATTTTTATAACTTTTTTCTAAAATTTAATA
5388540 TATTTTTAT-A-TTTTTTACTAAAATTTAATA
1 -ATTTTTATAACTTTTTT-CTAAAATTTAATA
5388570 ATTTTTA
1 ATTTTTA
5388577 GATTGTAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 6 0.19
29 17 0.53
30 9 0.28
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (30 bp):
ATTTTTATAACTTTTTTCTAAAATTTAATA
Found at i:5390578 original size:91 final size:92
Alignment explanation
Indices: 5390438--5390605 Score: 268
Period size: 91 Copynumber: 1.8 Consensus size: 92
5390428 TTTTGTTGCG
* * * *
5390438 TAGTATGCTTTTCACCTAAAATCGTGATTGTGTTATAAATTGAAATACTAAATGTATTTACAAAC
1 TAGTATGCTTTTCACCCAAAATCATGATTGTGTTATAAATTGAAATACTAAATGCAATTACAAAC
5390503 AATTACACTCAATTTTTTTTTATTTCA
66 AATTACACTCAATTTTTTTTTATTTCA
*
5390530 TAGTATG-TTTTCACCCAAAATCATGATTGT-TCTATAAATTGAAATACTAAGTGCAATTACAAA
1 TAGTATGCTTTTCACCCAAAATCATGATTGTGT-TATAAATTGAAATACTAAATGCAATTACAAA
5390593 CAATTACACTCAA
65 CAATTACACTCAA
5390606 ATTTAATTAC
Statistics
Matches: 70, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
90 1 0.01
91 62 0.89
92 7 0.10
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.39
Consensus pattern (92 bp):
TAGTATGCTTTTCACCCAAAATCATGATTGTGTTATAAATTGAAATACTAAATGCAATTACAAAC
AATTACACTCAATTTTTTTTTATTTCA
Found at i:5398341 original size:2 final size:2
Alignment explanation
Indices: 5398336--5398365 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5398326 ATAAATTTTA
5398336 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5398366 CTAAAAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5398991 original size:108 final size:109
Alignment explanation
Indices: 5398847--5399071 Score: 425
Period size: 108 Copynumber: 2.1 Consensus size: 109
5398837 TAGTATCATT
5398847 ATTAATTTTTATTTTTTCACTTTGACATTATATTATCCATCTTAAATTTCAAAACTATTAAAACT
1 ATTAATTTTTA-TTTTTCACTTTGACATTATATTATCCATCTTAAATTTCAAAACTATTAAAACT
5398912 CACCGTACATAAAAAAAATATTTGACATAAAAAATATATATCAAA
65 CACCGTACATAAAAAAAATATTTGACATAAAAAATATATATCAAA
5398957 ATTAATTTTTA-TTTTCACTTTGACATTATATTATCCATCTTAAATTTCAAAACTATTAAAACTC
1 ATTAATTTTTATTTTTCACTTTGACATTATATTATCCATCTTAAATTTCAAAACTATTAAAACTC
*
5399021 ACCGTACATAAAAAAAATATTTGACATATAAAATATATATCAAA
66 ACCGTACATAAAAAAAATATTTGACATAAAAAATATATATCAAA
5399065 ATTAATT
1 ATTAATT
5399072 GATATTTTAA
Statistics
Matches: 114, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
108 103 0.90
110 11 0.10
ACGTcount: A:0.44, C:0.13, G:0.03, T:0.40
Consensus pattern (109 bp):
ATTAATTTTTATTTTTCACTTTGACATTATATTATCCATCTTAAATTTCAAAACTATTAAAACTC
ACCGTACATAAAAAAAATATTTGACATAAAAAATATATATCAAA
Found at i:5399239 original size:26 final size:27
Alignment explanation
Indices: 5399186--5399240 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
5399176 AAATAAAATA
* * *
5399186 AAAAACTTAAAAATATGTTTGGTAATT
1 AAAAACTTAAAAATATATATGCTAATT
*
5399213 AAAAACTTAAAAATA-ATATGCTTATT
1 AAAAACTTAAAAATATATATGCTAATT
5399239 AA
1 AA
5399241 TTAAAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (27 bp):
AAAAACTTAAAAATATATATGCTAATT
Found at i:5419274 original size:16 final size:16
Alignment explanation
Indices: 5419253--5419288 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
5419243 GATTTGCTAT
5419253 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
5419269 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
5419285 TACA
1 TACA
5419289 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:5438286 original size:28 final size:29
Alignment explanation
Indices: 5438243--5438300 Score: 100
Period size: 28 Copynumber: 2.0 Consensus size: 29
5438233 TTCCTTATTA
*
5438243 TTTAAGTAAATAGATATTTATTATTTAAT
1 TTTAAGTAAATAGATATTTATTAATTAAT
5438272 TTTAAGTAAA-AGATATTTATTAATTAAT
1 TTTAAGTAAATAGATATTTATTAATTAAT
5438300 T
1 T
5438301 AATTATATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 18 0.64
29 10 0.36
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (29 bp):
TTTAAGTAAATAGATATTTATTAATTAAT
Found at i:5438811 original size:28 final size:29
Alignment explanation
Indices: 5438768--5438825 Score: 100
Period size: 28 Copynumber: 2.0 Consensus size: 29
5438758 TTCCTTATTA
*
5438768 TTTAAGTAAATAGATATTTATTATTTAAT
1 TTTAAGTAAATAGATATTTATTAATTAAT
5438797 TTTAAGTAAA-AGATATTTATTAATTAAT
1 TTTAAGTAAATAGATATTTATTAATTAAT
5438825 T
1 T
5438826 AATTATATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 18 0.64
29 10 0.36
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (29 bp):
TTTAAGTAAATAGATATTTATTAATTAAT
Done.